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Detailed information for vg1227342298:

Variant ID: vg1227342298 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 27342298
Reference Allele: AAlternative Allele: C
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 359. )

Flanking Sequence (100 bp) in Reference Genome:


AGAGCCATGGTTGACATTGAGCCAATCACAATGCCATTCAGGAAGTGCGATGTTTTGTTGTTGTTGATTGGTGAAACGCCTGTTTGCGACAGAGAGATGA[A/C]
ACCATCAGTTAGTCACACACACATTGCACCAAATTTGGTGAGAAGAGCTTCAACACTGAGAAGATGGCTTAGAAATGGAAGACTTGCCAGCTGAGGAGAG

Reverse complement sequence

CTCTCCTCAGCTGGCAAGTCTTCCATTTCTAAGCCATCTTCTCAGTGTTGAAGCTCTTCTCACCAAATTTGGTGCAATGTGTGTGTGACTAACTGATGGT[T/G]
TCATCTCTCTGTCGCAAACAGGCGTTTCACCAATCAACAACAACAAAACATCGCACTTCCTGAATGGCATTGTGATTGGCTCAATGTCAACCATGGCTCT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 66.70% 33.30% 0.00% 0.00% NA
All Indica  2759 97.80% 2.20% 0.00% 0.00% NA
All Japonica  1512 7.30% 92.70% 0.00% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 99.20% 0.80% 0.00% 0.00% NA
Indica II  465 98.70% 1.30% 0.00% 0.00% NA
Indica III  913 96.70% 3.30% 0.00% 0.00% NA
Indica Intermediate  786 97.60% 2.40% 0.00% 0.00% NA
Temperate Japonica  767 12.30% 87.70% 0.00% 0.00% NA
Tropical Japonica  504 0.80% 99.20% 0.00% 0.00% NA
Japonica Intermediate  241 5.40% 94.60% 0.00% 0.00% NA
VI/Aromatic  96 22.90% 77.10% 0.00% 0.00% NA
Intermediate  90 56.70% 43.30% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1227342298 A -> C LOC_Os12g44080.1 upstream_gene_variant ; 4518.0bp to feature; MODIFIER silent_mutation Average:59.338; most accessible tissue: Callus, score: 82.031 N N N N
vg1227342298 A -> C LOC_Os12g44100.1 downstream_gene_variant ; 3824.0bp to feature; MODIFIER silent_mutation Average:59.338; most accessible tissue: Callus, score: 82.031 N N N N
vg1227342298 A -> C LOC_Os12g44090.1 intron_variant ; MODIFIER silent_mutation Average:59.338; most accessible tissue: Callus, score: 82.031 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1227342298 NA 3.84E-29 mr1024 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1227342298 NA 4.81E-35 mr1542 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1227342298 NA 8.42E-13 mr1579 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1227342298 NA 1.37E-34 mr1670 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1227342298 NA 1.40E-13 mr1701 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1227342298 NA 8.75E-32 mr1922 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1227342298 NA 4.98E-12 mr1940 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1227342298 6.15E-06 4.72E-27 mr1024_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1227342298 NA 5.55E-15 mr1162_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1227342298 NA 3.92E-20 mr1657_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1227342298 NA 1.88E-30 mr1891_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1227342298 NA 7.01E-20 mr1922_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251